Locus 763

Sequence ID 2R_DroMel_CAF1
Location 3,690,817 – 3,690,975
Length 158
Max. P 0.581106
window1325 window1326

overview

Window 5

Location 3,690,817 – 3,690,936
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.79
Mean single sequence MFE -25.78
Consensus MFE -20.41
Energy contribution -21.85
Covariance contribution 1.44
Combinations/Pair 1.07
Mean z-score -1.54
Structure conservation index 0.79
SVM decision value 0.10
SVM RNA-class probability 0.581106
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3690817 119 - 20766785
UAUUAAUCAUUCUGAUUUGCAAAAGCGAACAACACUUCCAGCAAUUUCCGUUUAAGGGGAAGCUGAAA-AAACGUGCUGGUAGUAAGCGUUCGCUUAAUUAAAAUCGUGACAGGCAAGAA
......((((...(((((....((((((((...(((.((((((.((((.((((......)))).))))-.....)))))).)))....)))))))).....))))))))).......... ( -30.40)
>DroSec_CAF1 14562 120 - 1
UAUUAAUCAUUUCGAUUUGCAACAGCGAACAACACUUCCAGCAAUUUCCGUUUAAGGGGAAGCUGAAAAAAACGUGCUAGUAGUAAGCGUUCGCUUAAUUAAAAUCGUGACAGACAAGAA
......(((...((((((.....(((((((........((((..(..((......))..).))))..........(((.......))))))))))......))))))))).......... ( -27.40)
>DroEre_CAF1 10858 119 - 1
UAUUAAUCAUUCAGAAUUGCAAAAGCGAACAACACUUCCAGCAAUUUCCUUUUAAGGAGAAGCUGAAA-AAACGUGCUUGUAAGCGGCGUUCGCUUAAUUAAAAUCGUGACAGACAAGAA
......((..(((((.((....((((((((........((((..((((((....)))))).))))...-....(((((....))).)))))))))).....)).)).)))..))...... ( -25.80)
>DroYak_CAF1 10805 115 - 1
UAUUAAUCAUUCAGAAUUGCAAAA-CGAACAACACUUCCAGCAAUUUCCUUUUAAGGGGAAUCUGAAA-AAACGUGAUAGUAAG---CGUUCGCUUAAUUAAAAUCGUGACGGACAAGAA
......((.(((((((((((....-.(((......)))..)))))((((((....)))))))))))).-..(((......((((---(....)))))........))).........)). ( -19.54)
>consensus
UAUUAAUCAUUCAGAAUUGCAAAAGCGAACAACACUUCCAGCAAUUUCCGUUUAAGGGGAAGCUGAAA_AAACGUGCUAGUAAGAAGCGUUCGCUUAAUUAAAAUCGUGACAGACAAGAA
......((((...(((((....((((((((........((((..(((((......))))).))))..........(((.......))))))))))).....))))))))).......... (-20.41 = -21.85 +   1.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,690,857 – 3,690,975
Length 118
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 91.98
Mean single sequence MFE -25.40
Consensus MFE -20.02
Energy contribution -20.40
Covariance contribution 0.38
Combinations/Pair 1.06
Mean z-score -1.53
Structure conservation index 0.79
SVM decision value -0.05
SVM RNA-class probability 0.509882
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3690857 118 + 20766785
CCAGCACGUUU-UUUCAGCUUCCCCUUAAACGGAAAUUGCUGGAAGUGUUGUUCGCUUUUGCAAAUCAGAAUGAUUAAUAAUCCGAAUAUUUGUCAAACGUGAAUUCACUUUUCCCAUU
((((((.(((.-....)))((((........))))..))))))(((((..((((((.(((((((((......(((.....))).....))))).)))).)))))).)))))........ ( -26.80)
>DroSec_CAF1 14602 119 + 1
CUAGCACGUUUUUUUCAGCUUCCCCUUAAACGGAAAUUGCUGGAAGUGUUGUUCGCUGUUGCAAAUCGAAAUGAUUAAUAGUCCGAAUAUUUGUCAAACGUGAAUUCACUUUUCCCAUU
....(((((((((((((((((((........))))...))))))))...((((((((((((...(((.....)))))))))..))))))......)))))))................. ( -24.50)
>DroEre_CAF1 10898 118 + 1
CAAGCACGUUU-UUUCAGCUUCUCCUUAAAAGGAAAUUGCUGGAAGUGUUGUUCGCUUUUGCAAUUCUGAAUGAUUAAUAAUCCGAAUAUUUGUCAAACGUGAAUUCAUUUUUCCCAUU
....((((((.-.(((((....((((....))))((((((.(((((((.....))))))))))))))))))((((.((((.......)))).))))))))))................. ( -26.00)
>DroYak_CAF1 10842 117 + 1
CUAUCACGUUU-UUUCAGAUUCCCCUUAAAAGGAAAUUGCUGGAAGUGUUGUUCG-UUUUGCAAUUCUGAAUGAUUAAUAAUACGAAUAUUUGUCAAACGUGAAUUCACUUUUCCCGCA
...((((((((-((((((.((((........))))....))))))((((((((.(-((...((....))...))).))))))))...........))))))))................ ( -24.30)
>consensus
CUAGCACGUUU_UUUCAGCUUCCCCUUAAAAGGAAAUUGCUGGAAGUGUUGUUCGCUUUUGCAAAUCUGAAUGAUUAAUAAUCCGAAUAUUUGUCAAACGUGAAUUCACUUUUCCCAUU
....(((((((.(((((((((((........))))...)))))))....((((((...(((..((((.....))))..)))..))))))......)))))))................. (-20.02 = -20.40 +   0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:46:31 2006